\contentsline {section}{\numberline {1}Introduction}{3}
\contentsline {section}{\numberline {2}Getting Started}{4}
\contentsline {section}{\numberline {3}Simulation Framework}{4}
\contentsline {section}{\numberline {4}Class Breakdown}{5}
\contentsline {section}{\numberline {5}Interactions}{6}
\contentsline {subsection}{\numberline {5.1}Evolution of Cells: Mutation Types}{7}
\contentsline {subsection}{\numberline {5.2}Mathematical Model}{9}
\contentsline {subsection}{\numberline {5.3}Implementation}{12}
\contentsline {subsubsection}{\numberline {5.3.1}Protein-Protein Complex}{12}
\contentsline {section}{\numberline {6}Runge-Kutta Evaluation}{13}
\contentsline {subsection}{\numberline {6.1}Forming Derivatives: Using Node-Edge relationship to build a system of ODEs}{13}
\contentsline {subsection}{\numberline {6.2}Solving the ODE using Runge-Kutta}{14}
\contentsline {section}{\numberline {7}Scoring}{15}
\contentsline {subsection}{\numberline {7.1}Selection for Oscillitory Behavior}{15}
\contentsline {section}{\numberline {8}Output}{15}
\contentsline {subsection}{\numberline {8.1}Directory Structure}{15}
\contentsline {subsection}{\numberline {8.2}Data Plotting}{16}
\contentsline {section}{\numberline {9}Future Work}{16}
\contentsline {subsection}{\numberline {9.1}Version 1.0 Simplifications}{16}
\contentsline {subsection}{\numberline {9.2}Version 2.0 Planned Work}{17}
